name: data-and-storage
description: "Manage Galaxy datatypes, metadata, dataset storage, object stores,
file sources, data managers, tool data tables, and storage safety boundaries."
disable-model-invocation: true
metadata:
disco-role: operating
license: NOASSERTION
Galaxy Data and Storage
Use this sub-skill when a task involves Galaxy datatypes, sniffers, datatype metadata, dataset storage, object stores, file sources, data managers, tool data tables, .loc entries, or storage cleanup risk assessment.
Start Here
- For datatype implementation, registration, metadata, composite formats, and sniffer safety, read Data Formats.
- For data manager XML/JSON contracts and tool-data table entries, read Data Managers.
- For object-store, file-source, user template, credential, and storage-test planning, read Object Stores and Files.
- For common failures and conservative triage, read Troubleshooting.
- For a quick bounded-sniffer review, run
python scripts/check_datatype_sniffer.py PATH_OR_STDIN.
Routing Boundaries
- Stay here for datatype classes,
datatypes_conf.xml registration, sniff, set_meta, set_peek, data-manager outputs, tool-data tables, object-store configuration concepts, file-source credentials, dataset cleanup safety, and data/storage tests.
- Route broad Galaxy config placement, startup,
galaxy.yml editing, and admin deployment planning to Configuration and Admin.
- Route tool XML mechanics, wrapper tests, workflow YAML, and dependency declarations to Workflows and Tools.
- Route upload/download API calls, history dataset automation, and API-client scripting to API Automation.
Safety Defaults
- Never run cleanup, purge, migration, cloud object-store, or credentialed file-source actions without explicit user approval, target confirmation, backup/rollback context, and dry-run or read-only checks first.
- Treat sniffers as production hot paths: they must inspect bounded prefixes or bounded header/sample helpers, never entire files.
- Treat user file sources and object-store templates as secret-bearing configuration; do not print, persist, or invent credentials.
- Prefer local/unit tests and template/model validation before remote integration tests; skip cloud or network tests unless credentials and disposable resources are explicitly supplied.